library(bigMap)
source('~/bigMap/bdm_xtrs.R')
bdm.mybdm('~/omics/10xmouse/fitsne')
## [1] "~/omics/10xmouse/fitsne/"

FItSNE. Outputs

omics.class.legend(ncol = 8)

load('~/omics/10xmouse/fitsne/10x1M_nn50.RData')
load('~/omics/10xmouse/fitsne/10x1M_nn100.RData')
load('~/omics/10xmouse/fitsne/10x1M_nn200.RData')
load('~/omics/10xmouse/fitsne/10x1M_nn400.RData')
load('~/omics/10xmouse/fitsne/10x1M_nn800.RData')
load('~/omics/10xmouse/fitsne/10x1M_nn1600.RData')

Precision (beta) qMaps

k-ary neighbourhood preservation

omics.kn.plot(list(m.50, m.100, m.200, m.400, m.800, m.1600))

Running times

m.list <- list(m.50, m.100, m.200, m.400, m.800, m.1600)
r.times <- sapply(m.list, function(m) round(unlist(m$t) /60, 0))
r.times <- rbind(r.times, apply(r.times, 2, sum))
rownames(r.times) <- c('betas', 'ptsne', 'total')
colnames(r.times) <- sapply(m.list, function(m) m$Xbeta$ppx)
knitr::kable(r.times, caption = 'Computation times (min)') %>%
  kable_styling(full_width = F)
Computation times (min)
50 100 200 400 800 1600
betas 1 1 2 4 12 41
ptsne 3 3 4 6 9 14
total 4 4 6 10 21 55

Discussion